Publications by Stephen Turner
Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing
I haven’t posted much here recently, but here is a roundup of a few of the links I’ve shared on Twitter (@genetics_blog) over the last two weeks.Here is a nice tutorial on accessing high-throughput public data (from NCBI) using R and Bioconductor.Cloudnumbers.com, a startup that allows you to run high-performance computing (HPC) applications ...
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Sync Your Rprofile Across Multiple R Installations
Your Rprofile is a script that R executes every time you launch an R session. You can use it to automatically load packages, set your working directory, set options, define useful functions, and set up database connections, and run any other code you want every time you start R.If you’re using R in Linux, it’s a hidden file in you...
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I’m Starting a New Position at the University of Virginia
I just accepted an offer for a faculty position at the University of Virginia in the Center for Public Health Genomics / Department of Public Health Sciences. Starting in October I will be developing and directing a new centralized bioinformatics core in the UVA School of Medicine. Over the next few weeks I’m taking a much-needed va...
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GEO2R: Web App to Analyze Gene Expression in GEO Datasets Using R
Gene Expression Omnibus is NCBI’s repository for publicly available gene expression data with thousands of datasets having over 600,000 samples with array or sequencing data. You can download data from GEO using FTP, or download and load the data directly into R using the GEOquery bioconductor package written (and well documented) by Sean Davis...
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An example RNA-Seq Quality Control and Analysis Workflow
I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experiments using the FastX toolkit and FastQC.The second set (PDF) gives an example RNA-seq ...
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RNA-Seq & ChiP-Seq Data Analysis Course at EBI
I just got this announcement from EMBL-EBI about an RNA-seq/ChIP-seq analysis hands-on course. Find the full details, schedule, and speaker list here.Title: Advanced RNA-Seq and Chip-Seq Data Analysis Course Date: May 1-4 2012 Venue: EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK Registration Closing Date: March 6 2012 (12:00 midday GM...
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Query a MySQL Database from R using RMySQL
I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser’s public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame.Getting Genetics Done by Stephen Turner is licensed...
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New Year’s Resolution: Learn How to Code
Farhad Manjoo at Slate has a good article on why you need to learn how to program. Chances are, if you’re reading this post here you’re already fairly adept at some form of programming. But if you’re not, you should give it some serious thought.Gina Trapani, former editor of tech blog Lifehacker, is quoted in the article:“Lear...
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Annotating limma Results with Gene Names for Affy Microarrays
Lately I’ve been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won’t contain any featureData annotation. Consequentially, when I run topTable to get a list of differentially expressed genes, there’s no annotation information other than the...
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Hadley Wickham: ggplot2 Webinar (Today!)
Title: A Backstage Tour of ggplot2 with Hadley WickhamDate: Wednesday, February 8, 2012Time: 11:00AM – 12:00PM PacificPresenter: Hadley Wickham, Professor of Statistics, Rice UniversityRegister here.I used ggplot2 extensively a few years ago, but reverted back to base graphics when ggplot2 was too slow for a project I was working on. But ggplot...
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